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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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g_mmpbsa calculation #510

Closed dplizyy closed 4 years ago

dplizyy commented 6 years ago

Hi, developers of APBS,

Here I report a bug of APBS in reading PQR file.

I have some PQR files in ambPQR format. When I run APBS calculation, I got the following error information:

Parsing input file p2AaZppA.in... NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from p2AaZppA.pqr. Valist_readPQR: Error parsing atom 1! Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields. Error reading molecules!

After checking the PQR file, I found that the first and last residues'name were wrong in the PQR file:

ATOM 1 N NALA 192 -51.730-160.850 81.990 0.141 1.550 ATOM 2 H1 NALA 192 -50.730-160.800 82.120 0.200 1.200 ATOM 3 H2 NALA 192 -52.140-160.040 82.420 0.200 1.200 ATOM 4 H3 NALA 192 -51.990-161.700 82.470 0.200 1.200 ATOM 5 CA NALA 192 -52.130-160.830 80.570 0.096 1.700 ATOM 6 HA NALA 192 -51.570-161.650 80.140 0.089 1.200 ATOM 7 CB NALA 192 -51.670-159.560 79.850 -0.060 1.700 ATOM 8 HB1 NALA 192 -52.140-159.700 78.880 0.030 1.200 ATOM 9 HB2 NALA 192 -52.260-158.770 80.330 0.030 1.200 ATOM 10 HB3 NALA 192 -50.600-159.430 79.970 0.030 1.200 ATOM 11 C NALA 192 -53.620-161.060 80.360 0.616 1.700 ATOM 12 O NALA 192 -54.370-160.550 81.190 -0.572 1.520 ATOM 13 N PRO 193 -54.010-161.690 79.250 -0.255 1.550 ATOM 14 CD PRO 193 -53.210-162.380 78.260 0.019 1.700 . . . ATOM 3581 HE2 MET 422 -68.070-154.080 47.280 0.068 1.200 ATOM 3582 HE3 MET 422 -66.950-152.980 46.560 0.068 1.200 ATOM 3583 C MET 422 -71.000-158.100 45.100 0.597 1.700 ATOM 3584 O MET 422 -70.500-158.810 44.220 -0.568 1.520 ATOM 3585 N CASP 423 -72.210-157.550 44.990 -0.519 1.550 ATOM 3586 H CASP 423 -72.480-156.960 45.760 0.306 1.200 ATOM 3587 CA CASP 423 -72.990-157.520 43.760 -0.182 1.700 ATOM 3588 HA CASP 423 -72.710-158.360 43.130 0.105 1.200 ATOM 3589 CB CASP 423 -74.500-157.710 43.950 -0.068 1.700 ATOM 3590 HB1 CASP 423 -75.010-157.920 43.010 -0.021 1.200 ATOM 3591 HB2 CASP 423 -74.910-156.790 44.350 -0.021 1.200 ATOM 3592 CG CASP 423 -74.850-158.840 44.900 0.885 1.700 ATOM 3593 OD1 CASP 423 -74.440-159.970 44.570 -0.816 1.520 ATOM 3594 OD2 CASP 423 -75.600-158.630 45.890 -0.816 1.520 ATOM 3595 C CASP 423 -72.640-156.360 42.850 0.726 1.700 ATOM 3596 OC1 CASP 423 -72.580-156.480 41.600 -0.789 1.520 ATOM 3597 OC2 CASP 423 -72.380-155.260 43.370 -0.789 1.520 ATOM 3598 C7 LIG 424 -54.410-155.360 49.800 -0.267 1.700 ATOM 3599 C4 LIG 424 -54.560-156.630 50.140 -0.072 1.700 ATOM 3600 C3 LIG 424 -54.430-157.030 51.590 -0.296 1.700 ATOM 3601 C2 LIG 424 -53.550-158.280 51.780 0.345 1.700 ATOM 3602 C1 LIG 424 -53.900-159.420 50.820 -0.051 1.700

sobolevnrm commented 6 years ago

Hello --

I have Cc'ed some of the other developers for their help with this issue. I think the primary problem is the fact the coordinate fields run together. If you use the "add whitespace" option with PDB2PQR, it should resolve this issue.

Thank you,

Nathan

On Sat, Apr 7, 2018 at 7:52 PM, dplizyy notifications@github.com wrote:

Hi, developers of APBS,

Here I report a bug of APBS in reading PQR file.

I have some PQR files in ambPQR format. When I run APBS calculation, I got the following error information:

Parsing input file p2AaZppA.in... NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from p2AaZppA.pqr. Valist_readPQR: Error parsing atom 1! Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields. Error reading molecules!

After checking the PQR file, I found that the first and last residues'name were wrong in the PQR file:

ATOM 1 N NALA 192 -51.730-160.850 81.990 0.141 1.550 ATOM 2 H1 NALA 192 -50.730-160.800 82.120 0.200 1.200 ATOM 3 H2 NALA 192 -52.140-160.040 82.420 0.200 1.200 ATOM 4 H3 NALA 192 -51.990-161.700 82.470 0.200 1.200 ATOM 5 CA NALA 192 -52.130-160.830 80.570 0.096 1.700 ATOM 6 HA NALA 192 -51.570-161.650 80.140 0.089 1.200 ATOM 7 CB NALA 192 -51.670-159.560 79.850 -0.060 1.700 ATOM 8 HB1 NALA 192 -52.140-159.700 78.880 0.030 1.200 ATOM 9 HB2 NALA 192 -52.260-158.770 80.330 0.030 1.200 ATOM 10 HB3 NALA 192 -50.600-159.430 79.970 0.030 1.200 ATOM 11 C NALA 192 -53.620-161.060 80.360 0.616 1.700 ATOM 12 O NALA 192 -54.370-160.550 81.190 -0.572 1.520 ATOM 13 N PRO 193 -54.010-161.690 79.250 -0.255 1.550 ATOM 14 CD PRO 193 -53.210-162.380 78.260 0.019 1.700 . . . ATOM 3581 HE2 MET 422 -68.070-154.080 47.280 0.068 1.200 ATOM 3582 HE3 MET 422 -66.950-152.980 46.560 0.068 1.200 ATOM 3583 C MET 422 -71.000-158.100 45.100 0.597 1.700 ATOM 3584 O MET 422 -70.500-158.810 44.220 -0.568 1.520 ATOM 3585 N CASP 423 -72.210-157.550 44.990 -0.519 1.550 ATOM 3586 H CASP 423 -72.480-156.960 45.760 0.306 1.200 ATOM 3587 CA CASP 423 -72.990-157.520 43.760 -0.182 1.700 ATOM 3588 HA CASP 423 -72.710-158.360 43.130 0.105 1.200 ATOM 3589 CB CASP 423 -74.500-157.710 43.950 -0.068 1.700 ATOM 3590 HB1 CASP 423 -75.010-157.920 43.010 -0.021 1.200 ATOM 3591 HB2 CASP 423 -74.910-156.790 44.350 -0.021 1.200 ATOM 3592 CG CASP 423 -74.850-158.840 44.900 0.885 1.700 ATOM 3593 OD1 CASP 423 -74.440-159.970 44.570 -0.816 1.520 ATOM 3594 OD2 CASP 423 -75.600-158.630 45.890 -0.816 1.520 ATOM 3595 C CASP 423 -72.640-156.360 42.850 0.726 1.700 ATOM 3596 OC1 CASP 423 -72.580-156.480 41.600 -0.789 1.520 ATOM 3597 OC2 CASP 423 -72.380-155.260 43.370 -0.789 1.520 ATOM 3598 C7 LIG 424 -54.410-155.360 49.800 -0.267 1.700 ATOM 3599 C4 LIG 424 -54.560-156.630 50.140 -0.072 1.700 ATOM 3600 C3 LIG 424 -54.430-157.030 51.590 -0.296 1.700 ATOM 3601 C2 LIG 424 -53.550-158.280 51.780 0.345 1.700 ATOM 3602 C1 LIG 424 -53.900-159.420 50.820 -0.051 1.700

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dplizyy commented 6 years ago

However I didn't use PDB2PQR, I used a one step calculationcommand to calculate g_mmpbsa between receptor and ligand: g_mmpbsa -f md.xtc -s md.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp -tu ns If calculation was correct, I will obtain six files: energy_MM.xvg, contrib_MM.datpolar.xvg, contrib_pol.datapolar.xvg, contrib_apol.dat. But, now I got two additional files: pErjddLA.in and pErjddLA.pqr. So, I really don't know how to use the "add whitespace" option with PDB2PQR that you suggest method to resolve this issue. Could you teach me in detail? Thank you very much!

2018-04-09

lidongping1228

发件人：Nathan Baker notifications@github.com 发送时间：2018-04-09 11:08 主题：Re: [Electrostatics/apbs-pdb2pqr] g_mmpbsa calculation (#510) 收件人："Electrostatics/apbs-pdb2pqr"apbs-pdb2pqr@noreply.github.com 抄送："dplizyy"lidongping1228@sina.com,"Author"author@noreply.github.com

Hello --

I have Cc'ed some of the other developers for their help with this issue. I think the primary problem is the fact the coordinate fields run together. If you use the "add whitespace" option with PDB2PQR, it should resolve this issue.

Thank you,

Nathan

On Sat, Apr 7, 2018 at 7:52 PM, dplizyy notifications@github.com wrote:

Hi, developers of APBS,

Here I report a bug of APBS in reading PQR file.

I have some PQR files in ambPQR format. When I run APBS calculation, I got the following error information:

Parsing input file p2AaZppA.in... NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs NOsh: Deprecated use of ION keyword! Use key-value pairs Parsed input file. Got paths for 1 molecules Reading PQR-format atom data from p2AaZppA.pqr. Valist_readPQR: Error parsing atom 1! Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields. Error reading molecules!

After checking the PQR file, I found that the first and last residues'name were wrong in the PQR file:

ATOM 1 N NALA 192 -51.730-160.850 81.990 0.141 1.550 ATOM 2 H1 NALA 192 -50.730-160.800 82.120 0.200 1.200 ATOM 3 H2 NALA 192 -52.140-160.040 82.420 0.200 1.200 ATOM 4 H3 NALA 192 -51.990-161.700 82.470 0.200 1.200 ATOM 5 CA NALA 192 -52.130-160.830 80.570 0.096 1.700 ATOM 6 HA NALA 192 -51.570-161.650 80.140 0.089 1.200 ATOM 7 CB NALA 192 -51.670-159.560 79.850 -0.060 1.700 ATOM 8 HB1 NALA 192 -52.140-159.700 78.880 0.030 1.200 ATOM 9 HB2 NALA 192 -52.260-158.770 80.330 0.030 1.200 ATOM 10 HB3 NALA 192 -50.600-159.430 79.970 0.030 1.200 ATOM 11 C NALA 192 -53.620-161.060 80.360 0.616 1.700 ATOM 12 O NALA 192 -54.370-160.550 81.190 -0.572 1.520 ATOM 13 N PRO 193 -54.010-161.690 79.250 -0.255 1.550 ATOM 14 CD PRO 193 -53.210-162.380 78.260 0.019 1.700 . . . ATOM 3581 HE2 MET 422 -68.070-154.080 47.280 0.068 1.200 ATOM 3582 HE3 MET 422 -66.950-152.980 46.560 0.068 1.200 ATOM 3583 C MET 422 -71.000-158.100 45.100 0.597 1.700 ATOM 3584 O MET 422 -70.500-158.810 44.220 -0.568 1.520 ATOM 3585 N CASP 423 -72.210-157.550 44.990 -0.519 1.550 ATOM 3586 H CASP 423 -72.480-156.960 45.760 0.306 1.200 ATOM 3587 CA CASP 423 -72.990-157.520 43.760 -0.182 1.700 ATOM 3588 HA CASP 423 -72.710-158.360 43.130 0.105 1.200 ATOM 3589 CB CASP 423 -74.500-157.710 43.950 -0.068 1.700 ATOM 3590 HB1 CASP 423 -75.010-157.920 43.010 -0.021 1.200 ATOM 3591 HB2 CASP 423 -74.910-156.790 44.350 -0.021 1.200 ATOM 3592 CG CASP 423 -74.850-158.840 44.900 0.885 1.700 ATOM 3593 OD1 CASP 423 -74.440-159.970 44.570 -0.816 1.520 ATOM 3594 OD2 CASP 423 -75.600-158.630 45.890 -0.816 1.520 ATOM 3595 C CASP 423 -72.640-156.360 42.850 0.726 1.700 ATOM 3596 OC1 CASP 423 -72.580-156.480 41.600 -0.789 1.520 ATOM 3597 OC2 CASP 423 -72.380-155.260 43.370 -0.789 1.520 ATOM 3598 C7 LIG 424 -54.410-155.360 49.800 -0.267 1.700 ATOM 3599 C4 LIG 424 -54.560-156.630 50.140 -0.072 1.700 ATOM 3600 C3 LIG 424 -54.430-157.030 51.590 -0.296 1.700 ATOM 3601 C2 LIG 424 -53.550-158.280 51.780 0.345 1.700 ATOM 3602 C1 LIG 424 -53.900-159.420 50.820 -0.051 1.700

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kozlac commented 6 years ago

Hello @dplizyy , like @sobolevnrm said, the problem arises from the concatenated fields. You mentioned that you did not use PDB2PQR to obtain this file. Which software did you use?

dplizyy commented 6 years ago

APBS

2018-04-16

lidongping1228

发件人：Juan notifications@github.com 发送时间：2018-04-11 23:05 主题：Re: [Electrostatics/apbs-pdb2pqr] g_mmpbsa calculation (#510) 收件人："Electrostatics/apbs-pdb2pqr"apbs-pdb2pqr@noreply.github.com 抄送："dplizyy"lidongping1228@sina.com,"Mention"mention@noreply.github.com

Hello @dplizyy , like @sobolevnrm said, the problem arises from the concatenated fields. You mentioned that you did not use PDB2PQR to obtain this file. Which software did you use? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

sobolevnrm commented 4 years ago

The code is behaving as expected; the coordinates need to be separated by whitespace.